If it works, ignore the message. Rooting allows anyone to get into any secure folder, which is why you don't really have a "secure" folder any more.
If you want to restore it to unrooted,
first back everything up. See
Backing up an Android Device. Then follow
[Samsung] How to flash Stock ROM via ODIN to restore the phone to stock unrooted. Then restore everything that doesn't restore itself. (If you put your email address into the email app, it should restore your emails. If you've kept the default backing up of apps and data, it should restore your apps and their data. But you have it all backed up in case something doesn't restore by itself.)
Reflash the official firmware?
